A5014772607- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Cancer-related gene regulation
- Prenatal Screening and Diagnostics
- Fetal and Pediatric Neurological Disorders
- HIV Research and Treatment
- Fungal Biology and Applications
- Bacterial Genetics and Biotechnology
- Advanced biosensing and bioanalysis techniques
- CRISPR and Genetic Engineering
- Genomics and Chromatin Dynamics
- Microbial Natural Products and Biosynthesis
- Digestive system and related health
- Genomics and Phylogenetic Studies
- Antibiotic Resistance in Bacteria
- Enzyme Production and Characterization
- Microbial Metabolism and Applications
- DNA Repair Mechanisms
- Bacteriophages and microbial interactions
- DNA and Nucleic Acid Chemistry
- Gut microbiota and health
- Animal Genetics and Reproduction
- Cancer Genomics and Diagnostics
- Genetics and Neurodevelopmental Disorders
- Neuroblastoma Research and Treatments
Vilnius University
2013-2024
Czech Academy of Sciences, Institute of Biotechnology
2008
S-Adenosylmethionine-dependent DNA methyltransferases (MTases) perform direct methylation of cytosine to yield 5-methylcytosine (5mC), which serves as part the epigenetic regulation mechanism in vertebrates. Active demethylation 5mC by TET oxygenases produces 5-formylcytosine (fC) and 5-carboxylcytosine (caC), were shown be enzymatically excised then replaced with an unmodified nucleotide. Here we find that both bacterial mammalian C5-MTases can catalyze decarboxylation caC yielding vitro...
Sequence-specific derivatization: Enzymatic methylation of cytosine in DNA is part an epigenetic regulatory network vertebrates. In the absence cofactor S-adenosyl-L-methionine, bacterial cytosine-5 methyltransferases can catalyze condensation aliphatic thiols and selenols with 5-hydroxymethylcytosine, a recently discovered nucleobase mammalian DNA, to yield 5-chalcogenomethyl derivatives (see scheme). Detailed facts importance specialist readers are published as "Supporting Information"....
Type II restriction endonucleases (REases) cleave double-stranded DNA at specific sites within or close to their recognition sequences. Shortly after discovery in 1970, REases have become one of the primary tools molecular biology. However, list available specificities type is relatively short despite extensive search for them natural sources and multiple attempts artificially change specificity. In this study, we examined possibility generating cleavage by swapping putative target domains...
5-hydroxymethylcytosine (5hmC) is the most prevalent intermediate on oxidative DNA demethylation pathway and implicated in regulation of embryogenesis, neurological processes, cancerogenesis. Profiling this relatively scarce genomic modification clinical samples requires cost-effective high-resolution techniques that avoid harsh chemical treatment. Here, we present a bisulfite-free approach for 5hmC profiling at single-nucleotide resolution, named hmTOP-seq (5hmC-specific tethered...
Abstract Background Massively parallel sequencing of maternal cell-free DNA (cfDNA) is widely used to test fetal genetic abnormalities in non-invasive prenatal testing (NIPT). However, sequencing-based approaches are still high cost. Building upon previous knowledge that placenta, the main source circulating DNA, hypomethylated comparison tissue counterparts cfDNA, we propose targeting either unmodified or 5-hydroxymethylated CG sites specifically enriches material and reduces numbers...
ConspectusDNA is the genetic matter of life composed four major nucleotides which can be further furnished with biologically important covalent modifications. Among variety enzymes involved in DNA metabolism, AdoMet-dependent methyltransferases (MTases) combine recognition specific sequences and methylation a target nucleotide. The naturally transferred methyl groups play roles biological signaling, but they are poor physical reporters largely resistant to chemical derivatization. Therefore,...
Sequenzspezifische Derivatisierung: Die enzymatische Methylierung von Cytosin in DNA ist Bestandteil eines epigenetischen regulatorischen Netzwerks Wirbeltieren. In Abwesenheit des Methylierungs-Cofaktors S-Adenosyl-L-methionin können bakterielle Cytosin-5-methyltransferasen die Kondensation aliphatischen Thiolen und Selenolen mit 5-Hydroxymethylcytosin, einer kürzlich entdeckten Nukleobase Säuger-DNA, unter Bildung 5-Chalkogenmethyl-Derivaten katalysieren (siehe Schema). Detailed facts of...
Due to an extreme rarity of 5-carboxylcytosine (5caC) in the mammalian genome, investigation its role brings a considerable challenge. Methods based on bisulfite sequencing have been proposed for genome-wide 5caC analysis. However, bisulfite-based scarcely abundant demands significant experimental and computational resources, increasing cost. Here, we present bisulfite-free approach, caCLEAR, high-resolution mapping 5caCGs. The method uses atypical activity methyltransferase eM.SssI remove...
A two‐domain structure of the Type IIS restriction endonuclease MnlI has been identified by limited proteolysis. An N‐terminal domain enzyme mediates sequence‐specific interaction with DNA, whereas a monomeric C‐terminal resembles bacterial colicin nucleases in its requirement for alkaline earth as well transition metal ions double‐ and single‐stranded DNA cleavage activities. The results indicate that fusion non‐specific HNH‐type nuclease to binding had transformed into Mg 2+ ‐, Ni Co Mn Zn...
The formation of three oxidative DNA 5-methylcytosine (5mC) modifications (oxi-mCs)—5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC)—by the TET/JBP family dioxygenases prompted intensive studies their functional roles in mammalian cells. However, interplay these less abundant modified nucleotides other eukaryotic lineages remains poorly understood. We carried out a systematic study content distribution oxi-mCs RNA basidiomycetes Laccaria bicolor...
Neuroblastoma (NB) is a pediatric cancer of the developing sympathetic nervous system that exhibits significant variation in stage differentiation and cell composition tumors. Global loss DNA methylation genomic 5-hydroxymethylcytosine (5hmC) hallmark human cancers. Here, we used our recently developed single-base resolution approaches, hmTOP-seq uTOP-seq, for construction 5hmC maps identification large partially methylated domains (PMDs) different NB subpopulations. The profiles revealed...
Abstract Review: 84 refs.
We present a method, named Mx-TOP, for profiling of three epigenetic regulatory layers-chromatin accessibility, general DNA modification, and hydroxymethylation-from single library. The approach is based on chemo-enzymatic covalent tagging unmodified CG sites hydroxymethylated cytosine (5hmC) along with GC in chromatin, which are then mapped using tag-selective base-resolution TOP-seq sequencing. Our in-depth validation the revealed its sensitivity informativity evaluating chromatin...